Combined metabolome and transcriptome to analyze the regulatory network of key enzymes in the synthesis of senkirkine in Emilia sonchifolia.

Emilia sonchifolia (L.) DC. serves as a well-known folk medicinal and edible plant, yet its toxic component senkirkine exhibits hepatotoxicity. Acute high-dose exposure can induce sinusoidal obstruction syndrome, while chronic low-dose intake may cause hepatic megaloblastosis and fibrosis. This study applied metabolomics to analyze alkaloid compositions in the plant's roots, stems, leaves, and flowers. A total of 91 differential metabolites were detected, belonging to 10 alkaloids, among which pyrrolizidine alkaloids accounted for 13%. Senkirkine showed the most significant content variation between roots and flowers, with roots containing notably higher levels. Transcriptomic analysis identified 119,886 unigenes and 32,797 DEGs. Among these, authors selected 45 key enzymes involved in senkirkine biosynthesis, categorizing them into 7 groups corresponding to 172 candidate enzyme genes. Methyltransferase, alcohol dehydrogenase, acyltransferase, and cyclooxygenase genes expressed more highly in roots than in flowers, matching metabolomic expression patterns. Through qRT-PCR of five key enzyme genes, researchers found that four genes (BAHD-Ats, CCoAOMT, BOMT, 3AT) peaked in roots, while CAD showed highest expression in stems-findings consistent with transcriptomic results. This study provided references for gene functional expression analysis and laid a foundation for decoding the senkirkine biosynthesis pathway. It aims to regulate key enzyme genes to develop low-toxic E. sonchifolia resources, integrating metabolomic and transcriptomic approaches to balance medicinal efficacy and safety.